nextflow.config

// Configurable variables
params {
    joint = false
    
    // extract
    proportion_repeat = 0.8
    min_mapq = 40

    // call
    min_support = 5
    min_clip = 0
    min_clip_total = 0

    // merge
    window = -1

    // outliers
    control = []
    slop = 50
    min_clips = 0
    min_size = 0

    strling_call_outdir = './strling_call_results'
    outliers_outdir     = './outliers_results'
    str_index   = "$DATA/STRling/index/human_g1k_v38_decoy_phix_MASKED.fasta.str"
    reference   = "$DATA/Reference/GRCh38_masked/human_g1k_v38_decoy_phix_MASKED.fasta"
}

// set container values.
singularity {
    enabled = true
    runOptions ='-B /scratch/:/scratch -B /uufs/:/uufs'
    envWhitelist='APPS,UUFSCELL,DATA,USCRATCH,REPOSITORY,PROCESSING,ANALYSIS,SLURM_CPUS_ON_NODE,SLURM_JOB_ID,USER'
    autoMounts   = true
}

process {
    container = 'brwnj/strling:latest'
    errorStrategy = 'retry'
    maxRetries = 1
    executor = 'slurm'
    maxForks = 100
    clusterOptions = '-A ucgd-rw -p ucgd-rw --qos ucgd-prod-rw'
    //ext.args = "--dev"

    withName: strling_merge {
        errorStrategy = 'retry'
        maxRetries = 2
        time = 48.h
        memory = 120.GB
    }
    withName: strling_call {
        errorStrategy = 'retry'
        maxRetries = 2
        memory = { 4.GB * task.attempt }
    }
    withName: strling_outliers {
        errorStrategy = 'ignore'
    }
    withLabel: local {
        errorStrategy = 'retry'
        maxRetries = 2
        module = 'ucgd_modules'
        executor = 'local'
    }
}

trace {
    file = "STRling_trace.txt"
}